Academic researcher John Banks (not his real name) still has big personal regrets about bowing to pressure from his former university in the run-up to the government’s last high-stakes audit of research.

Universities obsess about the government’s Research Excellence Framework, known as the Ref, with good reason. The four-yearly exercise determines not only where around £2bn a year of public funding will go, but where universities and individual departments will rank in league tables.

As the 2014 submission deadline drew closer Banks was called into a meeting to discuss what publications he could enter to be judged. “To my horror they told me what I had was ‘slim pickings’. I was told to finish my two books quickly and to try to get more published after that,” he says.

“After a long illness my mum was at the end of her life, and I was needed to support her. By asking me to speed things up they were basically asking me to give up my private life.”

He explained he needed some personal time to be at the hospital, but says that, in the panic of the run-up to the submission date, his personal issues weren’t heard. “They were simply fixated with the Ref.”

“It was dizzying. I was told the university was depending on me turning this work out early. So I ended up next to my mum’s deathbed proofreading a monograph. The last conversation I had with her was about work and why I was doing so much.”

As a junior researcher who had netted a job in an intensely competitive academic market he says he was worried about whether his position would be safe if he didn’t deliver what was needed to help his department get a good Ref score. “I got it done,” he says quietly. “I felt regretful then, and I still feel regretful now about the time I lost with my family. And I probably stuffed up parts of those two books because I was hurrying and not entirely focused.”

I wish we could talk more openly about mental health in academia

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The daunting Ref cycle is starting to hot up in universities now. It is still two years until universities must submit their entries for the 2021 Ref. But institutions’ mock audits of staff are already under way – sometimes in secret. Academics warn the assessment is triggering a mental health crisis in universities. They say researchers are too afraid or ashamed to speak out about their anxiety and depression.

Dorothy Bishop, professor of developmental neuropsychology at Oxford University, and a member of the executive council of the Campaign for the Defence of British Universities, says: “The Ref was designed as a system to distribute funding, but it has turned into a fairly brutal management tool.”

She argues that the “endless” cycle of research assessment leaves many academics feeling completely inadequate. Universities often brand individual academics as “un-Ref-able”, because they haven’t published enough research papers in the most prestigious academic journals.

“Universities want top-rated 4* publications,” she explains. “But the reality is that a lot of academics are doing very respectable, useful work that isn’t at the forefront of the world. There is an implication that if you aren’t a top-flight researcher you are a second-class person.”

Dr Jason Scott-Warren, an English lecturer at Cambridge University, says: “The Ref values research that drives forward the cutting edge of the discipline, or research that makes a difference to public policy or the economy. But a lot of our research and writing is directed towards students – the next generation that we are meant to be nurturing. The Ref doesn’t care about them at all.”

Scott-Warren says he hates the audit because of the way it ramps up the anxiety of doing research and trying to get it published, and sours relations within departments.

“I’ve been quite fortunate, but I’ve heard a lot of horror stories about the pressures that people are under. People go into academia bright-eyed and optimistic but if they don’t produce to order they are quickly downgraded. You can be pouring your soul into your job but end up feeling utterly discouraged.”

Research published by the Royal Society and the Wellcome Trust last year found that academia is one of the worst careers for stress, with nearly four in ten academics suffering from mental health conditions. Many suffer in silence: about 37% have problems but only 6% disclose it to their university.

Joanna Waldie, a postdoctoral physics research fellow at Cambridge University, says that she loves research but has considered leaving for the sake of her wellbeing.

Waldie, who has had mental health problems since she was a teenager and had severe depression during her PhD, spoke about the stresses of her job at a workshop on tackling researchers’ mental health issues, co-hosted by the Royal Society and other learned societies.

She says: “As a researcher you have many demands on your time. For instance I train and guide PhD students and often need to fix things in the lab as technicians are very scarce in universities now. I am careful about my hours because of the health problems I have had in the past. I work about 45 hours a week, but I see colleagues working too many hours a week, in my view.”

She adds: “I do see a lot of researchers who are suffering from anxiety and depression, but people are not very open about their stresses. I think it would be a big step in the right direction if we talked about it more.”

Dr Charlotte Mathieson, a lecturer in English literature at Surrey University, who surveyed nearly 200 early career researchers after the last Ref, says: “I found that many were experiencing anxiety, depression and other mental health issues, in part because of the Ref, and exacerbated by being in precarious positions in an increasingly competitive job market.”

In UK universities there is a daily erosion of integrity | Stefan Collini

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Ref rules changed in November after an independent government review and a year of consultation. Universities now have to enter work from everyone doing a “significant” amount of research, rather than picking and choosing their best people.

The shame of not being selected may disappear, though there is speculation that universities may still game the system by giving more research time to their stars, and changing contracts to avoid entering others. Either way, Mathieson expects the stress for junior academics to be worse this time round because many more are now employed on casual short-term contracts.

She explains that universities want junior academics to prove they are doing research that will look good in the Ref before they give them a permanent job. “This is a huge pressure if you are trying to carve out time to do research in between teaching-heavy contracts and applying for jobs. It is very stressful not knowing where you will be living in six months and whether you will have a job.”

Dr James Thompson, a reader in modern British history at Bristol University, and vice president of the Bristol branch of the University and College Union, says: “Ref practices vary by university and department, but the sector-wide picture is of the Ref as a god that must be worshipped.”